Subject: Re: CCL:help: pdb --> charmm

From: Szilveszter Juhos <[email-masked]>
Date: Tue, 29 Jan 2002 12:22:46 +0000 (GMT)

On Mon, 28 Jan 2002, J. Zheng wrote:
> 1)   open read card unit 10 name 7LYZ.pdb 
>    when I type above command, charmm said there is no title.

Try run from script file, it will be more convenient. Prepare your file
like:

* This is a title, write here
* something useful and end with a line 
* with only asterix in it
*
! it is a comment

..do your stuff here... 

And run:

$ charmm.exe < infile.scr

But you will have problems with amino acids with undefined protonation
state if you are reading straight from PDB. If you do not have access to
Accelrys software/docs, try:

http://www.scripps.edu/brooks/

Hope it helps (I think starting with a smaller molecule would be easier).

Szilva